Project "Sign" is a US study of unidentifiable flying objects, "Sign" was one in a series of studies, "Sign" lived shortly before being dissolved, "Grudge" and "Blue Book" came thereafter. Blue Book had been operating for years before a termination order was given in 1969. Blue Book then ceased activity in 1970.

What if "Sign" and "Blue Book" found something else?

This is why both were terminated
What if they did find something else?
the foundation would shut them down

A: A visual illusion of disks in the sky, when you get closer to them, the illusion creates negative vacuum in the area surrounding it, burning organisms near the vacuum

B: A meme that burns items that subjects feel like are burning, this meme is activated by looking at anomalous disks of light, unable to physically touch them, turns up on radars

C: Actual spaceship, the ship is empty, entering it will cause the subject to control the ship with thoughts, spaceship also sends out a clone of you that never experienced this, the spaceship will burn all organisms near it when taking off. These spaceships move in fleets and can go lightspeed, liberty is stripped and all you can do is follow the fleet.

D: Something to do with actual aliens (Though I would put a unique idea on it)
Aliens that are… the ships themselves? Yeah, sentient (or sapient) disks that can fly at lightspeed, poses no threat. Occasionally comes to the ground and burns plants. Disks can be guided towards places.

^ Those are draft ideas, at the moment not very polished.
But hey, tell me what you think about the plot itself.
Had the idea looking up alien conspiracies and stuff

The IRL project seems like good inspiration for a skip, but so far the plot is "the government found something, and the Foundation covered it up." How do you plan to present that story - as a series of memos back and forth? action reports about raids? Both? Importantly, how are you going to end that story? The end is usually the part that tells you how the middle should be.

I think there's a way to execute this that makes it irrelevant what the alien actually is; you can look at SCP-3985 for a great example of how to show this kind of conflict playing out in a way that focuses on the administration and avoids saying what the entity is at all. That said, the idea that a meme or something is causing people to alter reality such that they're making the UFOs themselves sounds like the most promising of the ideas you have.

Ultimately, "what happened to sign and blue book" is just a starting point, so your next step is to think about how you want the story to look - what kind of stage you're trying to set up and what kind of action you want to take place there.

Containment procedures: Propaganda telling the public that aliens do not exist will be constantly shown. Should the question ever arise pertaining to disks of light in the sky, the anomaly must be explained, common explanations are weather balloons and refraction of light off of the earth's atmosphere. Should subjects be affected by the cognitohazard in an isolated area, OPERATION SPIRAL is to be executed. Areas with very little to no population are to be monitored by MTF Aleph-1 "Sign". In the even that a large amount of the population makes false and dangerous assumptions about SCP-XXXX after seeing it, COMMANDMENT GRUDGE is to be an order.

Discription: SCP-XXXX is an array of unidentified flying objects and is a cognitohazard that [DATA EXPUNGED]. What SCP-XXXX actually is [DATA EXPUNGED]. All other info on SCP-XXXX is reserved to use by MTF Aleph-2 "Blue Book"

Operation spiral: Basically where they take tranquilize the subject, check their background and if deemed dangerous, keep them in a comatose state until they are "needed" as sort of weapon.

COmmandment grudge: Basically drugging the water supply to stop the situation

*Raid log of blue book operations go here*

*Memos go here*

*Blue book operations file and research papers goes here*
(example operation) The subject has read books on aliens. When looking at disks every plant at the nearby area is burned and subject witnesses a spaceship fly away

or

subject does not know about aliens, reads a book on flying disks relating to earthquakes in the area, subject is exposed, minor earthquake occurs.

(insert Commandment "Belief" basically where they use the SCP as a weapon, a dangerous weapon)